Dear Matias,
Thank you very much for your detailed answer. I really appreciate the details you’ve provided.
It seems like, in my problem, I need to scale epsilon_ij for certain atom pairs while not changing the 1-4_epsilon_ij. One possible way I think would be to adjust the scnb parameters so that the 1-4_epsilon_ij for a pair of scaled epsilon_ij would be the same as unscaled epsilon_ij. I could be able to do this by editing the .dat files. I just have one more question: do you know if the SCNB and SCEE parameters are used for anything else than calculating the 1-4 interactions? In case they are used for calculating some other stuff, me changing them would not be good. I just want to cross-check this.
best,
Batuhan
> On 22 Oct 2020, at 16:43, Matias Machado <mmachado.pasteur.edu.uy> wrote:
>
> Dear Batuhan,
>
> You should ask the authors of the work, what does it exactly mean "The 1−4 nonbonded intra-molecular interactions were not altered"? Because it isn't completely clear to me.
>
> As I pointed before, 1-4 LJ terms are calculated from the combination rules like any other LJ pair interaction, but scaling the resulting well.
>
> Hence,
>
> 1-4_sigma(ij) = ( sigma(ii) + sigma(jj) )/2
> 1-4_epsilon(ij) = sqrt( epsilon(ii)*epsilon(jj)) ) / SCNB
>
> Notice that SCNB may be different according to the force field, e.g. in case of AMBER's proteins/dna/rna/lipids SCNB=2.0, but in GLYCAM SCNB=1.0.
>
> If you look at the file "GLYCAM_06EPb.dat" at section DIHEDRAL, then you'll see the specific definition of "SCEE=1.0 SCNB=1.0" after the periodicity of each term.
>
> So, one interpretation is that the authors didn't change the scaling factor (SCNB=1.0), which I guess is the most reasonably one. While the other possibility is they kept the same 1-4_epsilon(ij) value. As you can see, both options render complete different results...
>
> A possible workaround to keep the same 1-4_epsilon(ij) value without using changeLJ14Pair, could be setting the SCNB value so that the outcome remains the same as using the "old" LJ parameters. Yes, that will be a very tedious task!
>
> Regarding GROMACS implementation...
>
> First be aware that the present code of GROMACS can't handle setting multiple SCNB (or SCEE) parameters at the same time in a system, this is critical when combining GLYCAM force field with protein or other "AMBER force fields". The are some workarounds, see for example [https://doi.org/10.1016/j.softx.2019.100241 <https://doi.org/10.1016/j.softx.2019.100241>], but it isn't easy...
>
> Second, both AMBER and GROMACS build the 1-4 interactions in the same way, though combination rules and scaling factors. Providing you are using the right options in GROMCAS you should get the same result as in AMBER. So, this statement "changing the sigma/epsilon values for a given atom type at the [atomtypes] directive in Gromacs does not alter the calculated 1-4 interactions." is wrong, 1-4 interactions do change...
>
> Best,
>
> Matías
>
> ----- Mensaje original -----
> De: "Batuhan Kav" <bkavlist.gmail.com <mailto:bkavlist.gmail.com>>
> Para: "AMBER Mailing List" <amber.ambermd.org <mailto:amber.ambermd.org>>
> Enviados: Jueves, 22 de Octubre 2020 5:34:22
> Asunto: Re: [AMBER] Changing lj_radius without changing lj_14_radius
>
> Dear Matias,
>
> Thank you very much for your reply and I’m sorry for the cryptic question.
>
> I am essentially working on the implementation of a rather new version of the Glycam force field, which is described here: https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.6b00295 <https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.6b00295><https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.6b00295 <https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.6b00295>> . The strategy there is basically changing the epsilon values for some of the atom types while keeping the original 1-4 interactions intact (Sec. 4.2.2). So basically, vdW and Coulomb energy terms will be modified while 1-4 vdW and 1-4 Coulomb terms will remain the same.
>
> By using Parmed’s “addLJType” (as well as with changeLJType, got the same results) I make the modifications to the epsilon values. These modifications change the vdW energy values as well as the 1-4 vdW energies that I obtain from a single-step minimization, which I think is expected. However, to be consistent with the above proposed force field, I need to keep the 1-4 interactions the same. For instance, changing the sigma/epsilon values for a given atom type at the [atomtypes] directive in Gromacs does not alter the calculated 1-4 interactions. I was wondering if the same functionality exists in Amber.
>
> I cannot use changeLJ14Pair or similar commands because I obtain the topology using leap not with chamber.
>
> best,
> Batuhan
>
>
>> On 21 Oct 2020, at 20:25, Matias Machado <mmachado.pasteur.edu.uy> wrote:
>>
>> Dear Batuhan,
>>
>> I don't fully understand your question...
>>
>> The 1-4 LJ terms are the result of scaling the resulting LJ pair interaction by the SCNB factor.
>>
>> If you want to set new LJ parameters to each type, then look at keyword "changeLJSingleType". This will reset all corresponding LJ pair interactions (including 1-4 if any). To preserve the former 1-4 values, you can then use the keyword "changeLJ14Pair" to revert the previous effect on specific 1-4 LJ interactions (Note: it only works in chamber-created topologies, I've never used).
>>
>> If you want to set particular LJ pair paramters out of the combination rule but not to change the LJ of the type, then use keyword "changeLJPair". Only the LJ parameters of the selected pairs are affected (including 1-4 teres if any). Again, use keyword "changeLJ14Pair" to revert the effect on the 1-4 interactions.
>>
>> Best,
>>
>> Matias
>>
>> ------------------------------------
>> PhD.
>> Researcher at Biomolecular Simulations Lab.
>> Institut Pasteur de Montevideo | Uruguay
>> [http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
>> [http://www.sirahff.com]
>>
>> ----- Mensaje original -----
>> De: "Batuhan Kav" <bkavlist.gmail.com>
>> Para: "AMBER Mailing List" <amber.ambermd.org>
>> Enviados: Lunes, 19 de Octubre 2020 12:23:32
>> Asunto: [AMBER] Changing lj_radius without changing lj_14_radius
>>
>> Dear All,
>>
>> In my system, I’m trying to change the LJ parameters of certain atom types using Parmed’s addLJType command. However, while doing this I need to keep the 1-4 interactions unchanged. I’ve realized that, when I change the LJ radius/epsilon using the addLJType command, the 1-4 vdW energy (as the minimization output suggests) also changes and the radius_14 option in Parmed is only for the chamber-related topologies.
>>
>> Is there any way to accomplish this?
>>
>> thank you alll,
>> Batuhan
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
> http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
> http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 26 2020 - 09:30:02 PDT
